2019-08-28 15:02:47 +00:00
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<!DOCTYPE html>
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2020-04-27 20:35:41 +00:00
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<html>
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2019-08-28 15:02:47 +00:00
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<head>
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<meta charset="utf-8" />
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<meta name="generator" content="pandoc" />
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2020-04-27 20:35:41 +00:00
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<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
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2019-08-28 15:02:47 +00:00
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2023-01-03 19:23:06 +00:00
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<title> OMOP Common Data Model</title>
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2019-08-28 15:02:47 +00:00
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2023-01-03 19:23:06 +00:00
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<script src="site_libs/header-attrs-2.16/header-attrs.js"></script>
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2022-01-13 16:01:36 +00:00
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<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
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2019-08-28 15:02:47 +00:00
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
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<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
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<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
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<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
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2022-01-13 16:01:36 +00:00
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<style>h1 {font-size: 34px;}
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h1.title {font-size: 38px;}
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h2 {font-size: 30px;}
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h3 {font-size: 24px;}
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h4 {font-size: 18px;}
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h5 {font-size: 16px;}
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h6 {font-size: 12px;}
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code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
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pre:not([class]) { background-color: white }</style>
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2019-08-28 15:02:47 +00:00
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<script src="site_libs/navigation-1.1/tabsets.js"></script>
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<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
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2023-01-03 19:23:06 +00:00
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<script src="site_libs/htmlwidgets-1.5.4/htmlwidgets.js"></script>
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<script src="site_libs/calendar-binding-0.2.1/calendar.js"></script>
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<link href="site_libs/font-awesome-6.1.1/css/all.min.css" rel="stylesheet" />
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<link href="site_libs/font-awesome-6.1.1/css/v4-shims.min.css" rel="stylesheet" />
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<link href="site_libs/bttn-0.2.4/bttn.min.css" rel="stylesheet" />
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2019-08-28 15:02:47 +00:00
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<link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
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2021-01-06 15:52:57 +00:00
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<style type="text/css">
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code{white-space: pre-wrap;}
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span.smallcaps{font-variant: small-caps;}
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span.underline{text-decoration: underline;}
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div.column{display: inline-block; vertical-align: top; width: 50%;}
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div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
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ul.task-list{list-style: none;}
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</style>
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2019-08-28 15:02:47 +00:00
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<style type="text/css">code{white-space: pre;}</style>
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<script type="text/javascript">
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if (window.hljs) {
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</script>
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2021-01-06 15:52:57 +00:00
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2022-04-22 19:12:19 +00:00
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2019-08-28 15:02:47 +00:00
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<link rel="stylesheet" href="style.css" type="text/css" />
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<style type = "text/css">
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.main-container {
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max-width: 940px;
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margin-left: auto;
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margin-right: auto;
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}
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img {
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max-width:100%;
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}
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.tabbed-pane {
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padding-top: 12px;
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}
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.html-widget {
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margin-bottom: 20px;
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}
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button.code-folding-btn:focus {
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outline: none;
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}
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summary {
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display: list-item;
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}
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2022-04-22 19:12:19 +00:00
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details > summary > p:only-child {
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display: inline;
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}
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2022-01-13 16:01:36 +00:00
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pre code {
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padding: 0;
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}
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2019-08-28 15:02:47 +00:00
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</style>
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<style type="text/css">
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.dropdown-submenu {
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position: relative;
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}
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.dropdown-submenu>.dropdown-menu {
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top: 0;
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left: 100%;
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margin-top: -6px;
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margin-left: -1px;
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border-radius: 0 6px 6px 6px;
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}
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.dropdown-submenu:hover>.dropdown-menu {
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display: block;
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}
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.dropdown-submenu>a:after {
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display: block;
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content: " ";
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float: right;
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width: 0;
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height: 0;
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border-color: transparent;
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border-style: solid;
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border-width: 5px 0 5px 5px;
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border-left-color: #cccccc;
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margin-top: 5px;
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margin-right: -10px;
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}
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.dropdown-submenu:hover>a:after {
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2022-01-13 16:01:36 +00:00
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border-left-color: #adb5bd;
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2019-08-28 15:02:47 +00:00
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}
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.dropdown-submenu.pull-left {
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float: none;
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}
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.dropdown-submenu.pull-left>.dropdown-menu {
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left: -100%;
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margin-left: 10px;
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border-radius: 6px 0 6px 6px;
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}
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</style>
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2022-01-13 16:01:36 +00:00
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<script type="text/javascript">
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2019-08-28 15:02:47 +00:00
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// manage active state of menu based on current page
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$(document).ready(function () {
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// active menu anchor
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href = window.location.pathname
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href = href.substr(href.lastIndexOf('/') + 1)
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if (href === "")
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href = "index.html";
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var menuAnchor = $('a[href="' + href + '"]');
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2023-01-03 19:23:06 +00:00
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// mark the anchor link active (and if it's in a dropdown, also mark that active)
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var dropdown = menuAnchor.closest('li.dropdown');
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if (window.bootstrap) { // Bootstrap 4+
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menuAnchor.addClass('active');
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dropdown.find('> .dropdown-toggle').addClass('active');
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} else { // Bootstrap 3
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menuAnchor.parent().addClass('active');
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dropdown.addClass('active');
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}
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2022-01-13 16:01:36 +00:00
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// Navbar adjustments
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var navHeight = $(".navbar").first().height() + 15;
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var style = document.createElement('style');
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var pt = "padding-top: " + navHeight + "px; ";
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var mt = "margin-top: -" + navHeight + "px; ";
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var css = "";
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// offset scroll position for anchor links (for fixed navbar)
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for (var i = 1; i <= 6; i++) {
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css += ".section h" + i + "{ " + pt + mt + "}\n";
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}
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style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
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document.head.appendChild(style);
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2019-08-28 15:02:47 +00:00
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});
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</script>
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<!-- tabsets -->
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<style type="text/css">
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.tabset-dropdown > .nav-tabs {
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display: inline-table;
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max-height: 500px;
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min-height: 44px;
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overflow-y: auto;
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border: 1px solid #ddd;
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border-radius: 4px;
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}
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.tabset-dropdown > .nav-tabs > li.active:before {
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content: "";
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font-family: 'Glyphicons Halflings';
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display: inline-block;
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padding: 10px;
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border-right: 1px solid #ddd;
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}
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.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
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content: "";
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border: none;
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}
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.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
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content: "";
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font-family: 'Glyphicons Halflings';
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display: inline-block;
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padding: 10px;
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border-right: 1px solid #ddd;
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}
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.tabset-dropdown > .nav-tabs > li.active {
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display: block;
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}
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.tabset-dropdown > .nav-tabs > li > a,
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.tabset-dropdown > .nav-tabs > li > a:focus,
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.tabset-dropdown > .nav-tabs > li > a:hover {
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border: none;
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display: inline-block;
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border-radius: 4px;
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2020-04-27 20:35:41 +00:00
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background-color: transparent;
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2019-08-28 15:02:47 +00:00
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}
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.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
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display: block;
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float: none;
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}
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.tabset-dropdown > .nav-tabs > li {
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display: none;
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}
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</style>
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2020-04-27 20:35:41 +00:00
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<!-- code folding -->
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2019-08-28 15:02:47 +00:00
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2020-04-27 20:35:41 +00:00
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</head>
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<body>
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<div class="container-fluid main-container">
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2019-08-28 15:02:47 +00:00
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<div class="navbar navbar-default navbar-fixed-top" role="navigation">
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<div class="container">
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<div class="navbar-header">
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2022-04-22 19:12:19 +00:00
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<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-bs-toggle="collapse" data-target="#navbar" data-bs-target="#navbar">
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2019-08-28 15:02:47 +00:00
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<span class="icon-bar"></span>
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<span class="icon-bar"></span>
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<span class="icon-bar"></span>
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</button>
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<a class="navbar-brand" href="index.html"><div><img src="ohdsi16x16.png"></img> OMOP Common Data Model </div></a>
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</div>
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<div id="navbar" class="navbar-collapse collapse">
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<ul class="nav navbar-nav">
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<li>
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<a href="index.html">
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2023-01-03 19:23:06 +00:00
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<span class="fa fa-house"></span>
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2019-08-28 15:02:47 +00:00
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</a>
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</li>
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2021-02-19 02:37:32 +00:00
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<li class="dropdown">
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2022-04-22 19:12:19 +00:00
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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2022-01-13 16:01:36 +00:00
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<span class="fa fa-landmark"></span>
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2019-10-31 19:06:09 +00:00
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Background
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2021-02-19 02:37:32 +00:00
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<span class="caret"></span>
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2019-10-31 19:06:09 +00:00
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</a>
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2021-02-19 02:37:32 +00:00
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="background.html">Model Background</a>
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2021-02-19 02:37:32 +00:00
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<a href="vocabulary.html">How the Vocabulary is Built</a>
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Conventions
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<a href="ehrObsPeriods.html">Observation Periods for EHR Data</a>
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2022-07-27 01:48:28 +00:00
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CDM Proposals
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2019-10-31 19:06:09 +00:00
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<a href="cdmRequestProcess.html">How to Propose Changes to the CDM</a>
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2019-10-31 19:06:09 +00:00
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<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
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<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
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<a href="download.html">Download the DDL</a>
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2020-10-06 15:11:13 +00:00
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<li>
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2021-09-22 19:39:44 +00:00
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<a href="cdmRPackage.html">Use the CDM R Package</a>
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<li>
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<a href="drug_dose.html">Calculate Drug Dose</a>
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<a href="cdmDecisionTree.html">Help! My Data Doesn't Fit!</a>
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<a href="faq.html">FAQ</a>
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<a href="sqlScripts.html">SQL Scripts</a>
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2019-10-31 19:06:09 +00:00
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2023-01-03 19:23:06 +00:00
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<h1 class="title toc-ignore"><img src="ohdsi40x40.png"></img> OMOP
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Common Data Model</h1>
|
2019-08-28 15:02:47 +00:00
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</div>
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2023-01-03 19:23:06 +00:00
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<p>The Observational Medical Outcomes Partnership (OMOP) Common Data
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Model (CDM) is an open community data standard, designed to standardize
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the structure and content of observational data and to enable efficient
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analyses that can produce reliable evidence. A central component of the
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OMOP CDM is the OHDSI standardized vocabularies. The OHDSI vocabularies
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allow organization and standardization of medical terms to be used
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across the various clinical domains of the OMOP common data model and
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enable standardized analytics that leverage the knowledge base when
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constructing exposure and outcome phenotypes and other features within
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characterization, population-level effect estimation, and patient-level
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prediction studies.</p>
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<p>This website is meant to serve as a resource describing the
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specification of the available versions of the Common Data Model. This
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includes the structure of the model itself and the agreed upon
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conventions for each table and field as decided by the OHDSI Community.
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The vocabulary tables are part of the model and, as such, are detailed
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here. To download the vocabulary itself, please visit <a
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href="https://athena.ohdsi.org">https://athena.ohdsi.org</a>. For more
|
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information about the OHDSI suite of tools designed to implement best
|
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practices in characterization, population-level effect estimation and
|
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patient-level prediction, please visit <a
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href="https://ohdsi.github.io/Hades/">https://ohdsi.github.io/Hades/</a>.</p>
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<div id="the-cdm-working-group" class="section level2">
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<h2>The CDM Working Group</h2>
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<p>The CDM is managed by the OHDSI CDM Working Group. If you would like
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to join our group please fill out <a
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href="https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu">this
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form</a> and check “Common Data Model” to be added to our Microsoft
|
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Teams environment. This working group endeavors to maintain the OMOP CDM
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as a living model by soliciting and responding to requests from the
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community based on use cases and research purposes. For more information
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on the CDM refresh process please see the description <a
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href="http://ohdsi.github.io/CommonDataModel/cdmRefreshProcess.html">here</a>.
|
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You will find information on our meetings and links to join at the end
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of this page.</p>
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<div id="calendar" class="section level3">
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<h3>Calendar</h3>
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<p>This is the calendar of events for the CDM Working Group, including
|
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upcoming topics and links to meetings. If you would like to present to
|
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the group regarding a new use case for the OMOP CDM or if you would like
|
|
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the group’s assistance with a problem you are having, please fill out
|
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our sign-up form.</p>
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<p><a
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href="https://www.signupgenius.com/go/10C0948AEAD28A4F9CF8-workgroup"><img
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src="images/sign-up.png" style="width:15.0%" alt="Sign Up" /></a></p>
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<p><strong>Note</strong> If you do you have access to the OHDSI Teams
|
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|
|
Tenet, either contact Clair Blacketer at <a
|
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href="mailto:mblacke@its.jnj.com" class="email">mblacke@its.jnj.com</a>
|
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or fill out <a
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|
href="https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu">this
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form</a> and check “Common Data Model”</p>
|
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<script type="application/json" data-for="htmlwidget-2096806f57387e925ae8">{"x":{"options":{"defaultView":"month","taskView":false,"scheduleView":true,"useDetailPopup":true,"useCreationPopup":false,"isReadOnly":true,"usageStatistics":false,"month":{"startDayOfWeek":1,"narrowWeekend":true},"calendars":[{"id":1,"name":"PERSO","color":"#000","bgColor":"#c6d19d","borderColor":"forestgreen"},{"id":2,"name":"WORK","color":"#000","bgColor":"#F5A9A9","borderColor":"firebrick"},{"id":3,"name":"COURSES","color":"#000","bgColor":"#c6e2f6","borderColor":"#3b7cc6"}]},"schedules":[{"category":"time","dueDateClass":"","id":"scheduleca1b5497d5d1bc144191f2b3","calendarId":"1","title":"CDM WG Meeting","body":"","recurrenceRule":null,"start":"2023-01-03 10:00:00","end":"2023-01-03 11:00:00","location":"Teams: https://tinyurl.com/cdm1sttues","bgColor":null,"color":null,"borderColor":null},{"category":"time","dueDateClass":"","id":"schedule2e240e994b202048b6a0f29f","calendarId":"2","title":"CDM WG : Pregnancy","body":"The Pregnancy and Maternal Medicine working group will present.","recurrenceRule":null,"start":"2023-01-17 13:00:00","end":"2023-01-17 14:00:00","location":"Teams: https://tinyurl.com/cdm3rdtues","bgColor":null,"color":null,"borderColor":null},{"category":"time","dueDateClass":"","id":"schedule034876280bbb17a524c06ac9","calendarId":"1","title":"CDM WG Meeting : NLP","body":"The NLP working group will present some potential updates to the NOTE_NLP table.","recurrenceRule":null,"start":"2023-02-07 10:00:00","end":"2023-02-07 11:00:00","location":"Teams: https://tinyurl.com/cdm1sttues","bgColor":null,"color":null,"borderColor":null},{"category":"time","dueDateClass":"","id":"schedule00c06276293e04b2127f2068","calendarId":"2","title":"CDM WG Vocabulary Discussion","body":"Anna Ostropolets will join to ask us about our experiences using the OMOP Standard Vocabulary for ETL and other purposes","recurrenceRule":null,"start":"2023-02-21 13:00:00","end":"2023-02-21 14:00:00","location":"Teams: https://tinyurl.com/cdm3rdtues","bgColor":null,"color":null,"borderColor":null},{"category":"time","dueDateClass":"","id":"schedulec21692f529ac7db5d04c5ac0","calendarId":"1","title":"CDM WG : HADES","body":"Martijn Schuemie will present about the HADES working group and how their work interconnects with the OMOP CDM","recurrenceRule":null,"start":"2023-03-07 9:00:00","end":"2023-03-07 10:00:00","location":"Teams: https://tinyurl.com/cdm1sttues","bgColor":null,"color":null,"borderColor":null},{"category":"time","dueDateClass":"","id":"schedule5506afe3a3a0f6a29c758dad","calendarId":"2","title":"CDM WG Meeting","body":"","recurrenceRule":null,"start":"2023-03-21 13:00:00","end":"2023-03-21 14:00:00","location":"Teams: https://tinyurl.com/cdm3rdtues","bgColor":null,"color":null,"borderColor":null},{"category":"time","dueDateClass":"","id":"schedule3450081ddd59038a3c3e0749","calendarId":"1","title":"CDM WG Meeting","body":"","recurrenceRule":null,"start":"2023-04-04 10:00:00","end":"2023-04-04 11:00:00","location":"Teams: https://tinyurl.com/cdm1sttues","bgColor":null,"color":null,"borderColor":null},{"category":"time","dueDateClass":"","id":"scheduleab62c35a8b5abe22ac7cd62d","calendarId":"2","title":"CDM WG Meeting","body":"","recurrenceRule":null,"start":"2023-04-18 13:00:00","end":"2023-04-18 14:00:00","location":"Teams: https://tinyurl.com/cdm3rdtues","bgColor":null,"color":null,"borderColor":null},{"category":"time","dueDateClass":"","id":"schedule8416070f36e3b376232e958c","calendarId":"1","title":"CDM WG Meeting","body":"","recurrenceRule":null,"start":"2023-05-02 10:00:00","end":"2023-05-02 11:00:00","location":"Teams: https://tinyurl.com/cdm1sttues","bgColor":null,"color":null,"borderColor":null},{"category":"time","dueDateClass":"","id":"scheduleb60088b77b52b6220496807d","calendarId":"2","title":"CDM WG Meeting","body":"","recurrenceRule":null,"start":"2023-05-16 13:00:00","end":"2023-05-16 14:00:00","location":"Teams: https://tinyurl.com/cdm3rdtues","bgColor":null,"color":null,"borderColor":null},{"category":"time","dueDateClass":"","id":"sc
|
2023-01-03 19:23:06 +00:00
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</div>
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</div>
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2021-09-22 19:39:44 +00:00
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|
<div id="current-cdm-version" class="section level2">
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<h2>Current CDM Version</h2>
|
2023-01-03 19:23:06 +00:00
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<p>The current CDM version is <a
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|
href="http://ohdsi.github.io/CommonDataModel/cdm54.html">CDM v5.4</a>,
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depicted below. This CDM version was developed over the course of a year
|
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by considering requests that were sent via our <a
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href="https://github.com/OHDSI/CommonDataModel/issues">issues page</a>.
|
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The list of proposed changes was then shared with the community in
|
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|
multiple ways: through discussions at the weekly OHDSI Community calls,
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discussions with the OHDSI Steering Committee, and discussions with all
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potentially affected workgroups. The <a
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|
href="http://ohdsi.github.io/CommonDataModel/cdm54Changes.html">final
|
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changes</a> were then delivered to the Community through a new R package
|
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designed to dynamically generate the DDLs and documentation for all
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supported SQL dialects.</p>
|
2021-09-22 19:39:44 +00:00
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<ul>
|
2023-01-03 19:23:06 +00:00
|
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<li><a
|
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href="https://github.com/OHDSI/CommonDataModel/tree/v5.4.0/inst/ddl/5.4">Link
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to DDLs for CDM v5.4</a></li>
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<li><a
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href="https://github.com/OHDSI/CommonDataModel/tree/master#readme">Link
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to ReadMe for instructions on how to use the R package</a></li>
|
2021-09-22 19:39:44 +00:00
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</ul>
|
2022-01-13 18:59:03 +00:00
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<p><img src="images/cdm54.png" /> <br></p>
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<div id="current-support-for-cdm-v5.4" class="section level3">
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<h3>Current Support for CDM v5.4</h3>
|
2023-01-03 19:23:06 +00:00
|
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<p>The table below details which OHDSI tools support CDM v5.4. There are
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two levels of support: legacy support means that the tool supports all
|
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tables and fields that were present in CDM v5.3 and feature support
|
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indicates that the tool supports any new tables and fields in CDM v5.4
|
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that were not present in CDM v5.3. A green check ✅ indicates that the
|
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|
support level for the listed tool is in place, has been tested, and
|
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|
|
released. A warning sign ⚠️ indicates that the support level for the
|
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listed tool has been initiated but has not yet been tested and released.
|
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|
<br></p>
|
2022-01-13 18:59:03 +00:00
|
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|
<table>
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<colgroup>
|
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<col width="25%" />
|
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<col width="25%" />
|
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<col width="25%" />
|
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<col width="25%" />
|
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</colgroup>
|
|
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|
|
|
<thead>
|
|
|
|
|
|
<tr class="header">
|
|
|
|
|
|
<th><strong>Tool</strong></th>
|
|
|
|
|
|
<th><strong>Description</strong></th>
|
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|
|
|
|
<th><strong>Legacy Support</strong></th>
|
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|
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|
|
<th><strong>Feature Support</strong></th>
|
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|
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|
</tr>
|
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|
</thead>
|
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|
|
<tbody>
|
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|
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|
<tr class="odd">
|
|
|
|
|
|
<td><strong>CDM R package</strong></td>
|
2023-01-03 19:23:06 +00:00
|
|
|
|
<td>This package can be downloaded from <a
|
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|
|
|
|
href="https://github.com/OHDSI/CommonDataModel/">https://github.com/OHDSI/CommonDataModel/</a>.
|
|
|
|
|
|
It functions to dynamically create the OMOP CDM documentation and DDL
|
|
|
|
|
|
scripts to instantiate the CDM tables.</td>
|
2022-01-17 18:29:26 +00:00
|
|
|
|
<td>✅</td>
|
|
|
|
|
|
<td>✅</td>
|
2022-01-13 18:59:03 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="even">
|
|
|
|
|
|
<td><strong>Data Quality Dashboard</strong></td>
|
2023-01-03 19:23:06 +00:00
|
|
|
|
<td>This package can be downloaded from <a
|
|
|
|
|
|
href="https://github.com/OHDSI/DataQualityDashboard">https://github.com/OHDSI/DataQualityDashboard</a>.
|
|
|
|
|
|
It runs a set of > 3500 data quality checks against an OMOP CDM
|
|
|
|
|
|
instance and is required to be run on all databases prior to
|
|
|
|
|
|
participating in an OHDSI network research study.</td>
|
2022-01-17 18:29:26 +00:00
|
|
|
|
<td>✅</td>
|
|
|
|
|
|
<td>⚠️</td>
|
2022-01-13 18:59:03 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd">
|
|
|
|
|
|
<td><strong>Achilles</strong></td>
|
2023-01-03 19:23:06 +00:00
|
|
|
|
<td>This package can be downloaded from <a
|
|
|
|
|
|
href="https://github.com/OHDSI/Achilles">https://github.com/OHDSI/Achilles</a>,
|
|
|
|
|
|
performing a set of broad database characterizations agains an OMOP CDM
|
|
|
|
|
|
instance.</td>
|
2022-01-17 18:29:26 +00:00
|
|
|
|
<td>✅</td>
|
|
|
|
|
|
<td>⚠️</td>
|
2022-01-13 18:59:03 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="even">
|
|
|
|
|
|
<td><strong>ARES</strong></td>
|
2023-01-03 19:23:06 +00:00
|
|
|
|
<td>This package can be downloaded from <a
|
|
|
|
|
|
href="https://github.com/OHDSI/Ares">https://github.com/OHDSI/Ares</a>
|
|
|
|
|
|
and is designed to display the results from both the ACHILLES and
|
|
|
|
|
|
DataQualityDashboard packages to support data quality and
|
|
|
|
|
|
characterization research.</td>
|
2022-01-17 18:29:26 +00:00
|
|
|
|
<td>✅</td>
|
|
|
|
|
|
<td>⚠️</td>
|
2022-01-13 18:59:03 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd">
|
|
|
|
|
|
<td><strong>ATLAS</strong></td>
|
2023-01-03 19:23:06 +00:00
|
|
|
|
<td>ATLAS is an open source software tool for researchers to conduct
|
|
|
|
|
|
scientific analyses on standardized observational data. <a
|
|
|
|
|
|
href="http://atlas-demo.ohdsi.org/">Demo</a></td>
|
2022-01-17 18:29:26 +00:00
|
|
|
|
<td>✅</td>
|
|
|
|
|
|
<td>⚠️</td>
|
2022-01-13 18:59:03 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="even">
|
|
|
|
|
|
<td><strong>Rabbit-In-A-Hat</strong></td>
|
2023-01-03 19:23:06 +00:00
|
|
|
|
<td>This package can be downloaded from <a
|
|
|
|
|
|
href="https://github.com/OHDSI/WhiteRabbit">https://github.com/OHDSI/WhiteRabbit</a>
|
|
|
|
|
|
and is an application for interactive design of an ETL to the OMOP
|
|
|
|
|
|
Common Data Model with the help of the the scan report generated by
|
|
|
|
|
|
White Rabbit.</td>
|
2022-01-17 18:29:26 +00:00
|
|
|
|
<td>✅</td>
|
|
|
|
|
|
<td>✅</td>
|
2022-01-13 18:59:03 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="odd">
|
|
|
|
|
|
<td><strong>Feature Extraction</strong></td>
|
2023-01-03 19:23:06 +00:00
|
|
|
|
<td>This package can be downloaded from <a
|
|
|
|
|
|
href="https://github.com/OHDSI/FeatureExtraction">https://github.com/OHDSI/FeatureExtraction</a>.
|
|
|
|
|
|
It is designed to generate features (covariates) for a cohort generated
|
|
|
|
|
|
using the OMOP CDM.</td>
|
2022-01-17 18:29:26 +00:00
|
|
|
|
<td>✅</td>
|
|
|
|
|
|
<td>✅*</td>
|
2022-01-13 18:59:03 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr class="even">
|
|
|
|
|
|
<td><strong>Cohort Diagnostics</strong></td>
|
2023-01-03 19:23:06 +00:00
|
|
|
|
<td>This package can be downloaded from <a
|
|
|
|
|
|
href="https://github.com/OHDSI/CohortDiagnostics">https://github.com/OHDSI/CohortDiagnostics</a>
|
|
|
|
|
|
and is used to critically evaluate cohort phenotypes.</td>
|
2022-01-17 18:29:26 +00:00
|
|
|
|
<td>✅</td>
|
|
|
|
|
|
<td>⚠️</td>
|
2022-01-13 18:59:03 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
</tbody>
|
|
|
|
|
|
</table>
|
2023-01-03 19:23:06 +00:00
|
|
|
|
<p><br> * The <strong>Feature Extraction</strong> package supports all
|
|
|
|
|
|
relevant new features in CDM v5.4. For example, it was decided that,
|
|
|
|
|
|
from a methodological perspective, the EPISODE and EPISODE_EVENT tables
|
|
|
|
|
|
should not be included to define cohort covariates because the events
|
|
|
|
|
|
that make up episodes are already pulled in as potential covariates.</p>
|
2022-01-13 18:59:03 +00:00
|
|
|
|
<p><br></p>
|
|
|
|
|
|
</div>
|
2019-10-31 19:06:09 +00:00
|
|
|
|
<div id="cdm-wg-important-links" class="section level3">
|
|
|
|
|
|
<h3>CDM WG Important Links</h3>
|
2019-08-28 15:02:47 +00:00
|
|
|
|
<ul>
|
2023-01-03 19:23:06 +00:00
|
|
|
|
<li><a
|
|
|
|
|
|
href="https://drive.google.com/open?id=1DaNKe6ivIAZPJeI31VJ-pzNB9wS9hDqu">Google
|
|
|
|
|
|
Drive Location</a></li>
|
|
|
|
|
|
<li><a
|
|
|
|
|
|
href="https://docs.google.com/document/d/1WgKePjrI_cGdqn2XQCe1JdGaTzdMqU4p5ihkMt8fcAc/edit?usp=sharing">Running
|
|
|
|
|
|
Agenda</a></li>
|
|
|
|
|
|
<li><a href="https://github.com/OHDSI/CommonDataModel">CDM
|
|
|
|
|
|
Github</a></li>
|
|
|
|
|
|
<li><a
|
|
|
|
|
|
href="http://ohdsi.github.io/CommonDataModel/cdmRefreshProcess.html">Process
|
|
|
|
|
|
for adopting CDM and Vocabulary changes</a></li>
|
2019-08-28 15:02:47 +00:00
|
|
|
|
</ul>
|
|
|
|
|
|
</div>
|
2021-06-03 14:45:05 +00:00
|
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|
</div>
|
2019-08-28 15:02:47 +00:00
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</div>
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<script>
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// add bootstrap table styles to pandoc tables
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function bootstrapStylePandocTables() {
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2021-01-06 15:52:57 +00:00
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$('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
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2019-08-28 15:02:47 +00:00
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}
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$(document).ready(function () {
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bootstrapStylePandocTables();
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});
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</script>
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2020-04-27 20:35:41 +00:00
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<!-- tabsets -->
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<script>
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$(document).ready(function () {
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window.buildTabsets("TOC");
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});
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$(document).ready(function () {
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$('.tabset-dropdown > .nav-tabs > li').click(function () {
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2022-01-13 16:01:36 +00:00
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$(this).parent().toggleClass('nav-tabs-open');
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2020-04-27 20:35:41 +00:00
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});
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});
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</script>
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<!-- code folding -->
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2019-08-28 15:02:47 +00:00
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